Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019

Falk Schreiber; Björn Sommer; Gary D Bader; Padraig Gleeson; Martin Golebiewski; Michael Hucka; Sarah M Keating; Matthias König; Chris Myers; David Nickerson; Dagmar Waltemath

doi:10.1515/jib-2019-0035

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019

J Integr Bioinform. 2019 Jul 13;16(2):20190035. doi: 10.1515/jib-2019-0035.

Authors

Falk Schreiber^{1

2}, Björn Sommer¹, Gary D Bader³, Padraig Gleeson⁴, Martin Golebiewski⁵, Michael Hucka⁶, Sarah M Keating⁷, Matthias König⁸, Chris Myers⁹, David Nickerson¹⁰, Dagmar Waltemath¹¹

Affiliations

¹ Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.
² Faculty of IT, Monash University, Clayton, Australia.
³ The Donnelly Centre, University of Toronto, Toronto, Canada.
⁴ Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK.
⁵ Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.
⁶ California Institute of Technology, Pasadena, CA, USA.
⁷ Heidelberg University, Heidelberg, Germany.
⁸ Humboldt-University Berlin, Berlin, Germany.
⁹ University of Utah, Salt Late City, UT, USA.
¹⁰ Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand.
¹¹ University Medicine Greifswald, Greifswald, Germany.

Abstract

This special issue of the Journal of Integrative Bioinformatics presents an overview of COMBINE standards and their latest specifications. The standards cover representation formats for computational modeling in synthetic and systems biology and include BioPAX, CellML, NeuroML, SBML, SBGN, SBOL and SED-ML. The articles in this issue contain updated specifications of SBGN Process Description Level 1 Version 2, SBML Level 3 Core Version 2 Release 2, SBOL Version 2.3.0, and SBOL Visual Version 2.1.

Publication types

Review

MeSH terms

Computer Simulation*
Models, Biological*
Programming Languages*
Synthetic Biology*
Systems Biology*

Abstract

Publication types

MeSH terms

Grants and funding